To me, the whole idea about retro magazines is to read about the games and consoles you miss from years past. Putting up magazines talking about the PS2, Gamecube, and Xbox doesn't seem very retro, as the site name suggests, and next fall (2010), the Xbox 360 would be in that mix. Things that current are not retro. I personally don't consider the Saturn, N64 or PSone retro either, but they haven't been current for a long while now that they can actually be missed.
That's not to say that the scanned magazines will be deleted (they'll be removed for downloading, but as far as I know the scanned work will be kept for a later date), nor will people who have the print magazines get rid of them because of the new cut off date (hopefully they won't).
It is also a sort of goodwill gesture towards publishers that the site in no way intends to encroach on their business. No magazine currently offers back issues that are more than a few years old, and certainly none offer any from the 90's. So if the site doesn't step on any of their toes, they are more likely to look the other way than to hassle the site. Originally it was going to be a 10-year cut off date that moved up every year, but having a firm year as the cut off date seemed like a better idea.
The most important thing is that the old stuff is all still available